From 97689451ed678590cad5eb47a2d5b02c61232247 Mon Sep 17 00:00:00 2001 From: Akash Goel Date: Sun, 6 Sep 2026 23:11:58 -0700 Subject: [PATCH] Fix typos in the documentation --- docs/tutorials/theoryMP.md | 2 +- paper/paper.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/tutorials/theoryMP.md b/docs/tutorials/theoryMP.md index 019905f..1570f93 100644 --- a/docs/tutorials/theoryMP.md +++ b/docs/tutorials/theoryMP.md @@ -14,7 +14,7 @@ that is, the constraint force $f$ on $s$ is given by the Lagrange multiplier whi $$ W(x)=\int_{x_0}^{x} \mathrm{d} x' \; f(x') $$ -done to move the atom, or subset of atoms, along the pulling coordinate. Note that in the follwing we use the notations $f(x) \equiv f(t(x))$ interchangeable. +done to move the atom, or subset of atoms, along the pulling coordinate. Note that in the following we use the notations $f(x) \equiv f(t(x))$ interchangeable. diff --git a/paper/paper.md b/paper/paper.md index e43ac23..54f9b58 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -97,7 +97,7 @@ Each trajectory contains the constraint force $f(t)$ from which the work along t `dcTMD` provides plotting tools for work distribution analysis, free-energy $\Delta G(x)$ and friction profiles $\Gamma(x)$. #### 4. Example -![Figures crated using data taken from @Wolf2020_MultisecondDissociation of trypsin-benzamidine unbinding. a)-c) work distribution analysis. d) Decomposition of mean work $W_{\rm mean} = \langle W(x) \rangle$ into free energy $\Delta G(x)$ and dissipation work $W_{\rm diss}(x)$. e) non-equilibrium friction coefficient $\Gamma (x)$ along the pulling coordinate $x$.](figures/image2.png){width=\linewidth} +![Figures created using data taken from @Wolf2020_MultisecondDissociation of trypsin-benzamidine unbinding. a)-c) work distribution analysis. d) Decomposition of mean work $W_{\rm mean} = \langle W(x) \rangle$ into free energy $\Delta G(x)$ and dissipation work $W_{\rm diss}(x)$. e) non-equilibrium friction coefficient $\Gamma (x)$ along the pulling coordinate $x$.](figures/image2.png){width=\linewidth} Figure 1 displays a common analysis of a set of unbinding trajectories from TMD simulations of the trypsin-benzamidine complex [@Wolf2020_MultisecondDissociation]. The analysis of the work distribution displays good agreement with a normal distribution at two different evaluated positions of the pulling coordinate $x$. The mean work $W_{\rm mean} = \langle W(x) \rangle$, which shows no features on its own, yields a free energy profile $\Delta G(x)$, which displays a clearly defined transition state at $x \approx 0.45$ nm as well as a bound state in form of a free energy minimum at $x \approx 0.0$ nm and an unbound continuum for $x > 0.6$ nm. The maximum in friction $\Gamma$ around $x = 0.5$ nm is indicative of changes in the hydration of both ligand and binding site.